Sebastien, I think this may be related to the patch applied to fix Bug #1085320: the Gnome folks have since reverted (at least parts of) it (see Gnome bug 688808 [1]) because it caused custom icons to be shown as thumbnails, hence the borders reported in this LP bug. I tested this by applying the changes in [2] to current Nautilus in Raring (1:3.6.3-0ubuntu16), and the borders around my customized icons went away. Also, though I didn’t test very extensively, this didn’t result in desktop files again having borders as originally reported in #1085320.

(The commit log entry of [2] refers to [3], but I think it should refer to [4] instead.)

*[1] https://bugzilla.gnome.org/show_bug.cgi?id=688808#short_desc_nonedit_display
*[2] https://git.gnome.org/browse/nautilus/commit/?h=gnome-3-6&id=f69e472263b0bf6e1cc60c0eeaf7874fc7931f8d
*[3] https://git.gnome.org/browse/nautilus/commit/?id=d9ef715ea11e92917414d5d7bddd4dd1487fac1b
*[4] https://git.gnome.org/browse/nautilus/commit/?h=gnome-3-6&id=6cde4c5a6d639c85df09b8992a307f91d6b056a6